Journal Article

TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration

Lin Himmelmann and Dirk Metzler

in Bioinformatics

Volume 25, issue 18, pages 2440-2441
Published in print September 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp417
TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration

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Motivation: For the estimation of phylogenetic trees from molecular data, it is worthwhile to take prior paleontologic knowledge into account, if available. To calibrate the branch lengths of the tree with times assigned to geo-historical events or fossils, it is necessary to select a relaxed molecular clock model to specify how mutation rates can change along the phylogeny.

Results: We present the software TreeTime for Bayesian phylogeny estimation. It can take prior information about the topology of the tree and about branching times into account. Several relaxed molecular clock models are implemented in TreeTime. TreeTime is written in C++ and designed to be efficient and extensible.

Availability: TreeTime is freely available from http://evol.bio.lmu.de/statgen/software/treetime under the terms of the GNU General Public Licence (GPL, version 3 or later).

Contact: lin@linhi.de; metzler@bio.lmu.de

Journal Article.  1309 words. 

Subjects: Bioinformatics and Computational Biology

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